Run ID: SRR25827799
Sample name:
Date: 16-03-2024 09:01:58
Number of reads: 5340333
Percentage reads mapped: 98.52
Strain: lineage4.8
Drug-resistance: XDR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | R | rpoB p.Ser450Leu (1.00) |
Isoniazid | R | katG p.Ser315Thr (1.00) |
Ethambutol | R | embB p.Met306Val (1.00) |
Pyrazinamide | R | pncA p.Asp63Gly (1.00) |
Streptomycin | R | rpsL p.Lys43Arg (1.00) |
Fluoroquinolones | R | gyrA p.Asp94Ala (1.00) |
Moxifloxacin | R | gyrA p.Asp94Ala (1.00) |
Ofloxacin | R | gyrA p.Asp94Ala (1.00) |
Levofloxacin | R | gyrA p.Asp94Ala (1.00) |
Ciprofloxacin | R | gyrA p.Asp94Ala (1.00) |
Aminoglycosides | ||
Amikacin | ||
Capreomycin | ||
Kanamycin | ||
Cycloserine | ||
Ethionamide | ||
Clofazimine | ||
Para-aminosalicylic_acid | ||
Delamanid | ||
Bedaquiline | ||
Linezolid | R | rplC p.Cys154Arg (1.00) |
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage4 | Euro-American | LAM;T;S;X;H | None | 1.0 |
lineage4.8 | Euro-American (mainly T) | T1;T2;T3;T5 | RD219 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7582 | p.Asp94Ala | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 1.0 | streptomycin |
rplC | 801268 | p.Cys154Arg | missense_variant | 1.0 | linezolid |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2289054 | p.Asp63Gly | missense_variant | 1.0 | pyrazinamide |
embB | 4247429 | p.Met306Val | missense_variant | 1.0 | ethambutol |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 5332 | c.93C>T | synonymous_variant | 0.99 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 8168 | p.Glu289Asp | missense_variant | 1.0 |
rpoC | 765804 | p.Thr812Ile | missense_variant | 1.0 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpR5 | 779130 | c.144dupC | frameshift_variant | 0.57 |
mmpR5 | 779359 | c.371dupC | frameshift_variant | 0.18 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrl | 1474001 | n.344C>T | non_coding_transcript_exon_variant | 1.0 |
inhA | 1673406 | c.-796C>G | upstream_gene_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
PPE35 | 2168149 | p.Pro822Ser | missense_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
fprA | 3474934 | p.Arg310Gly | missense_variant | 0.99 |
clpC1 | 4039729 | p.Asp326Asn | missense_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4245417 | p.Gly729Arg | missense_variant | 1.0 |
ubiA | 4269296 | p.Met180Val | missense_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |